
% PG (final)
@Article{eberle2017,
   Author="Eberle, M. A.  and Fritzilas, E.  and Krusche, P.  and K{\"a}llberg, M.  and Moore, B. L.  and Bekritsky, M. A.  and Iqbal, Z.  and Chuang, H. Y.  and Humphray, S. J.  and Halpern, A. L.  and Kruglyak, S.  and Margulies, E. H.  and McVean, G.  and Bentley, D. R. ",
   Title="{{A} reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree}",
   doi = {10.1101/gr.210500.116},
   url = {http://dx.doi.org/10.1101/gr.210500.116},
   Journal="Genome Res.",
   Year="2017",
   Volume="27",
   Number="1",
   Pages="157--164",
   Month="Jan"
}

% PG (pre-print)
@article {pgPreprint,
	author = {Eberle, Michael A and Fritzilas, Epameinondas and Krusche, Peter and K{\"a}llberg, Morten and Moore, Benjamin L and Bekritsky, Mitchell A and Iqbal, Zamin and Chuang, Han-Yu and Humphray, Sean J and Halpert, Aaron L and Kruglyak, Semyon and Margulies, Elliott H and McVean, Gil and Bentley, David R},
	title = {A reference dataset of 5.4 million human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree},
	year = {2016},
	doi = {10.1101/055541},
	publisher = {Cold Spring Harbor Labs Journals},
	URL = {http://biorxiv.org/content/early/2016/05/26/055541},
	eprint = {http://biorxiv.org/content/early/2016/05/26/055541.full.pdf},
	journal = {bioRxiv}
}

% 11504945 
@Article{pevzner2001,
   Author="Pevzner, P. A.  and Tang, H.  and Waterman, M. S. ",
   Title="{{A}n {E}ulerian path approach to {D}{N}{A} fragment assembly}",
   Journal="Proc. Natl. Acad. Sci. U.S.A.",
   Year="2001",
   Volume="98",
   Number="17",
   Pages="9748--9753",
   Month="Aug"
}

@article{lesne2009,
  title = {Entropy estimation of very short symbolic sequences},
  author = {Lesne, Annick and Blanc, Jean-Luc and Pezard, Laurent},
  journal = {Phys. Rev. E},
  volume = {79},
  issue = {4},
  pages = {046208},
  numpages = {10},
  year = {2009},
  month = {Apr},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevE.79.046208},
  url = {https://link.aps.org/doi/10.1103/PhysRevE.79.046208}
}

@ARTICLE{ziv1977,
    author = {Jacob Ziv and Abraham Lempel},
    title = {A universal algorithm for sequential data compression},
    journal = {IEEE TRANSACTIONS ON INFORMATION THEORY},
    year = {1977},
    volume = {23},
    number = {3},
    pages = {337--343}
}

% Scikit-learn:
@article{scikit-learn,
 title={Scikit-learn: Machine Learning in {P}ython},
 author={Pedregosa, F. and Varoquaux, G. and Gramfort, A. and Michel, V.
         and Thirion, B. and Grisel, O. and Blondel, M. and Prettenhofer, P.
         and Weiss, R. and Dubourg, V. and Vanderplas, J. and Passos, A. and
         Cournapeau, D. and Brucher, M. and Perrot, M. and Duchesnay, E.},
 journal={Journal of Machine Learning Research},
 volume={12},
 pages={2825--2830},
 year={2011}
}

% GATK 'framework' paper (see https://software.broadinstitute.org/gatk/documentation/topic?name=faqs for other citeable GATK papers)
@article{depristo2011,
  abstract = {Recent advances in sequencing technology make it possible to comprehensively catalog genetic variation in population samples, creating a foundation for understanding human disease, ancestry and evolution. The amounts of raw data produced are prodigious, and many computational steps are required to translate this output into high-quality variant calls. We present a unified analytic framework to discover and genotype variation among multiple samples simultaneously that achieves sensitive and specific results across five sequencing technologies and three distinct, canonical experimental designs. Our process includes (i) initial read mapping; (ii) local realignment around indels; (iii) base quality score recalibration; (iv) SNP discovery and genotyping to find all potential variants; and (v) machine learning to separate true segregating variation from machine artifacts common to next-generation sequencing technologies. We here discuss the application of these tools, instantiated in the Genome Analysis Toolkit, to deep whole-genome, whole-exome capture and multi-sample low-pass ($\sim$4x) 1000 Genomes Project datasets.},
  added-at = {2014-10-13T22:39:22.000+0200},
  author = {DePristo, Mark A and Banks, Eric and Poplin, Ryan and Garimella, Kiran V and Maguire, Jared R and Hartl, Christopher and Philippakis, Anthony A and del Angel, Guillermo and Rivas, Manuel A and Hanna, Matt and McKenna, Aaron and Fennell, Tim J and Kernytsky, Andrew M and Sivachenko, Andrey Y and Cibulskis, Kristian and Gabriel, Stacey B and Altshuler, David and Daly, Mark J},
  biburl = {https://www.bibsonomy.org/bibtex/2bf1ad7b095c81c93a2557f005866f5c3/peter.ralph},
  comment = {10.1038/ng.806},
  interhash = {7f2f8a812e6577947a017acdc8bdf0c5},
  intrahash = {bf1ad7b095c81c93a2557f005866f5c3},
  issn = {10614036},
  journal = {Nat Genet},
  keywords = {GATK SNP_calling genotyping genotyping_error methods short_read_data software},
  month = may,
  number = 5,
  pages = {491--498},
  publisher = {Nature Publishing Group},
  timestamp = {2014-10-13T22:39:22.000+0200},
  title = {A framework for variation discovery and genotyping using next-generation {DNA} sequencing data},
  url = {http://dx.doi.org/10.1038/ng.806},
  volume = 43,
  year = 2011
}

% Freebayes pre-print
@ARTICLE{garrison2012,
    author = {{Garrison}, E. and {Marth}, G.},
    title = "{Haplotype-based variant detection from short-read sequencing}",
    journal = {ArXiv e-prints},
    archivePrefix = "arXiv",
    eprint = {1207.3907},
    primaryClass = "q-bio.GN",
    keywords = {Quantitative Biology - Genomics, Quantitative Biology - Quantitative Methods},
    year = 2012,
    month = jul,
    adsurl = {http://adsabs.harvard.edu/abs/2012arXiv1207.3907G},
    adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}

% platypus
@Article{rimmer2014,
    Author="Rimmer, A.  and Phan, H.  and Mathieson, I.  and Iqbal, Z.  and Twigg, S. R. F.  and Wilkie, A. O. M.  and McVean, G.  and Lunter, G. ",
    Title="{{I}ntegrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications}",
    Journal="Nat. Genet.",
    Year="2014",
    Volume="46",
    Number="8",
    Pages="912--918",
    Month="Aug"
}

% 24307552
@Article{tigra2014,
    Author="Chen, K.  and Fan, X.  and Wallis, J.  and Ding, L.  and Weinstock, G. ",
    Title="{{T}IGRA: a targeted iterative graph routing assembler for breakpoint assembly}",
    Journal="Genome Res.",
    Year="2014",
    Volume="24",
    Number="2",
    Pages="310--317",
    Month="Feb"
}
